Worries and Wonders
by crimeseriesfan
Summary: Basically, my take on what went on in Brennan's mind during the last two episodes of season 6, and on what happened off-screen. It is mostly an attempt to explore Brennan's worries, but it definitely includes some sweet moments between our beloved characters. Will be two chapters, one for each episode.
1. Chapter 1

_So, it's been ages since I've written anything, mostly because I was deeply horrified by the stories I wrote when I was like 14/15 years old. But I'd like to think that since I've gotten older, I've also gotten a little wiser. Hence, I decided to give writing a try again._

 _I was re-watching the last two episodes of season 6 for the millionth time (they're among my favorite episodes of the entire series), and I couldn't help but envision scenarios of the parts we didn't get to see, as well as think about what was going through Brennan's mind throughout these episodes. I'm a psychology student, so stuff like this interests me endlessly. You might see that in the story, as it's mostly an attempt to get at Brennan's underlying thoughts throughout the episodes. However, there are some sweet moments between Booth and Brennan included, obviously. Still, it might not be everyone's cup of tea, but I do hope some of you will enjoy reading this as much as I did writing it._

 _I divided the story into two chapters, one for each episode. I will post the second chapter soon, it just needs a little editing._

 _Obviously, I don't own Bones, nor any of the characters. Any mistakes are all mine though._

* * *

 **Chapter 1 – 6x22 "The Hole in the Heart"**

"Can I just…"

"Yeah, that's why I'm here".

Brennan laid her head on Booth's chest and cried like she hadn't in a very long time. Poor Vincent. Sweet, goofy, poor Vincent. For a while, all she could think about were his last moments, the way he had begged her not to make him leave. But maybe Booth was right. Maybe he wasn't talking to her, but to the universe, or whatever entity he believed in, to please not let him die. And he did say that he had loved it here. Whether he meant being alive or being at the Jeffersonian, that comforted Brennan a little. At least he had been happy.

Then, Brennan's thoughts shifted. She noted how comfortable she was not just lying on Booth's chest, but also in opening up to him about her thoughts and feelings. She went back to the night they acknowledged that there was something between them, that perhaps they could be together at a future time. Maybe that time was now. Vincent's death had put things in perspective for sure, but if she was being honest with herself, the last of her imperviousness had been gone for a while now. And maybe she was just imagining it, but it seemed that Booth was no longer angry. She looked up at him, bracing herself to ask him. But when their eyes met, it seemed that they had been thinking about the same thing. Something shifted between them in that moment. It was as if everything that had hung between them lately finally cleared up.

Still, Brennan was unsure if she should make a move. She had never been the best at reading people's emotions and thoughts. If she got this wrong, she could ruin what they had.

But before she could fully finish her train of thought and withdraw from him, his hand palmed her face and his lips were on hers. It was very gentle, but oh so good. They had kissed a few times before over the years, but this time felt different. This was not just a drunken or a desperate kiss, but a kiss full of emotion. It was real.

And this must have been what Sweets had been talking about, that dam breaking after they kissed. It didn't happen the other times, because it wasn't right. But now it was. They pulled apart, but not for long. The dam was broken. Their lips were back on each other's, not gentle anymore now, but full of passion. That passion fueled them and soon, all sadness of earlier was gone, leaving only lust, want, and perhaps even love.

* * *

Brennan woke the next morning with her head tucked in Booth's neck and her arm slung around his waist. She pulled back slightly to look up at his sleeping face, and couldn't help but smile. Last night had been amazing. It started out full of sadness and grief, but had ended in pure bliss. She knew she'd been right when they were stuck in that elevator a while ago and she'd said they would be very compatible. She chuckled. They were very compatible indeed.

Booth awoke too, roused by the slight movement she'd made. He looked at her, moved a strand of hair away from her face, and smiled. "Good morning, Bones. What were you laughing about?"

Brennan returned the smile. "Good morning to you too, Booth." Her eyes sparkled. "I was just thinking that I was right all those weeks ago. We are quite compatible."

Booth laughed out loud at that. "That's a bit of an understatement, Bones, but yeah, it was amazing." He grew more serious then. "Listen, I know that there is a lot we need to talk about, but right now I have to focus all my energy and attention on catching Broadsky. I just don't want you to think that this was just a one-time thing, or that it didn't mean anything to me, okay? Because it meant the world. I need you to know that."

"I know, Booth. And I understand. Broadsky is your priority now, as he should be. We can talk later."

Booth smiled gave Brennan a quick kiss. "Great, thanks Bones. Now, let's get ready, we have a big day ahead of us."

* * *

Brennan had been distracted all day. Thoughts of Vincent were mingling with thoughts of her night with Booth, and it made it hard to focus on her work. Of course, Angela picked up on it right away. Brennan debated whether she should tell her best friend about Booth, given that she and Booth hadn't even had a chance to talk yet. But Ange was her best friend, and maybe talking to her would help settle her mind a bit.

"… and, I got into bed with Booth last night."

At first, Angela didn't speak. Brennan wondered why not. She figured her best friend would have been ecstatic to hear the news, but maybe she no longer thought her and Booth getting together was a good idea.

"Why aren't you saying anything?" She eventually asked, part curious and part afraid of the answer.

"Because I don't want to yell "Hallelujah" so close to losing Vincent," Angela replied.

This answer settled Brennan's mind a bit, glad that Angela was indeed happy for her. But it also stirred something worrisome.

"I think I did it because of Vincent." Sure, last night felt so right, but what if she did it for all the wrong reasons?

Angela's voice interrupted Brennan's thoughts. "Wait, whoa, wha- what exactly happened after you- after you crawled into bed with Booth?"

Brennan couldn't help but let out a small laugh as she remembered that night. What happened was… amazing.

Just then, Hodgins entered, clearly having something to share, but Angela made him leave right away. When he was gone again, Brennan voiced her earlier concerns about why last night had happened last night.

"Ange, what if- what if my reasons for doing it were wrong? What if we've just laid a completely wrong foundation for something that should have been completely right?"

"Oh sweetie, no, don't think like that. What happened between you and Booth was beautiful, and it was a long time coming. So who cares what the exact circumstances or reasons were for it to happen last night? All that matters is that you and Booth have been chasing each other for a long time, and last night, you finally caught each other."

Brennan still wasn't quite convinced. "You really think that?"

"Yes, of course. Now, stop worrying and give me all the juicy details. It wasn't just you two who have been waiting a long time for this to happen, you know."

Angela was right, of course. And so Brennan told her all, well almost all, about what exactly had happened that night. And for a while, it made her happy. But still, her worries weren't completely gone, and they remained in the back of her mind for the remainder of the day.

* * *

That night, they sent Vincent off, back to his home country and to his mother. Despite singing "the Lime and the Coconut", which lightened the mood a little, it was all very sad, and Brennan was glad to have Booth there for comfort. She linked her arm through his, and after saying goodbye to the others, they left together. As they walked to his car, however, her worries about why exactly last night had happened came back in full force. Despite her earlier assurance to Booth that this would not be just a fling, she was feeling very overwhelmed by the idea of talking about being in a committed relationship. She stopped dead in her tracks.

Booth looked at her. "Bones, you okay?"

"No, I am not, actually. I know we said we would talk after we got Broadsky, but I don't think I can do that right now. With Vincent dying, it's all just too much. I- I need some time to figure things out."

She saw the hurt look on Booth's face, so she tried to ease his mind a little and took his hand in hers. "I am not running away from you, Booth, I promise. I won't need long. I'm just afraid I will ruin what we have before it even has a chance to unfold if… if I don't get all my ducks in a row, as you like to say. So, please, just give me a little time. Can you do that?"

Booth sighed. "Fine. Let me know when you're ready to talk, okay? I'll be waiting. I'm not giving up on you, on us."

"Good, because neither am I," Brennan replied. She kissed Booth briefly, before letting go of his hand. "Will I still see you tomorrow at work?" She asked hopefully.

"Yeah, see you tomorrow."

And with that, they each went their separate ways.

* * *

 _That's it for now, I hope you guys enjoyed it. Any feedback, either positive or negative, is welcome. Like I said, it's been a while since I've written anything so I might be a little rusty, and I'm always looking to improve my writing. Also, this chapter was quite short, but the next one will be a little longer, as I feel that most of the development of the story actually took place more in the last episode._

 _Stay tuned for the next chapter!_


	2. Chapter 2

_Hey guys,_

 _Thanks so much for the reviews and the favs & follows, it's great to see that you are enjoying my work. I've been really busy the past week, but I finally managed to find time to edit this chapter and post it._

 _This chapter focuses a little more on Brennan's thoughts in existing scenes than the previous one. I tried to link this to small things I picked up on in the episode, so the way Brennan's thoughts evolve are a representation of what I thought I saw in the episode, not necessarily how I would've imagined it in a perfect, joyful scenario. In a perfect world, Booth and Brennan would have gotten together right after "that night", but with the vibes coming off them in the last episode, I always felt that this was not the case. I hope I've done their story justice with this interpretation, and that it makes for a good read._

* * *

 **Chapter 2 – 6x23 "The Change in the Game"**

A few weeks went by, but Booth and Brennan never talked. Not about what happened the night after Vincent died and what it meant, anyway. They had a few cases in the mean while, and Brennan told herself that she simply hadn't had the time to talk to Booth. But if she was being completely honest, she just didn't know what to say or do. Things had become a little awkward between the two of them, and Brennan wasn't sure how to break through that. Before she could start working that out however, they got another case.

As it turns out, it wasn't just any case. Someone on Max' bowling team was killed. Naturally, she and Booth went to see Max to make sure he didn't kill the guy. He didn't, but suggested that she and Booth go undercover to figure out who did. Brennan was a little scared that it might be too awkward, spending a lot of time together without having talked about what was going on between them.

And then Booth suggested she play his girlfriend while undercover. Brennan was a bit taken aback by that. Of course, it made the most sense for their undercover work, but it also raised questions about their real-life situation that she couldn't quite answer. Was she actually his girlfriend? About to be? Or was it never going to happen? She didn't know just yet. So she said the only thing she could think of at the moment.

"Fine."

* * *

They had a few hours before they were expected at the bowling alley, so Brennan went home to find some appropriate undercover clothes and a few other things. As she was going through her bathroom dresser to get some make-up, she came across her period supplies. She disregarded them at first, until she realized that she hadn't needed those in a while. A thought occurred to her, but she didn't want to acknowledge it just yet. She couldn't be. She checked the calendar on her phone, where she kept meticulous track of everything. She went back a few weeks, and then a few more, until she came across her last period. Almost seven weeks ago.

She had never been late before.

Crap. How had she not realized this sooner? She was always so careful. But then again, they hadn't been very careful the night they slept together, and she hadn't been fully focused the weeks afterwards, what with everything going on. Brennan checked her watch. She still had some time left before she had to meet Booth. She left the bathroom, grabbed her keys, and went to the nearest pharmacy. She had to know for sure, and she had to know now.

She came back home with three different pregnancy tests, each claiming to have a good accuracy rate and to pick up on early pregnancy. She took all three of them, and sat down on her bed when she was done, laying the sticks out next to her. She set an alarm on her phone and for the next few minutes, her thoughts went all over the place. What if she was indeed pregnant? How would Booth feel about that? They hadn't even talked about being together, let alone raising a child together. Also, Booth had already had one child out of wedlock. Could he handle a situation like that again? Would they actually become a couple, or simply co-parent without starting a relationship? What if she was not pregnant? If she had to admit it to herself, that would make her a little sad. The prospect of having a child actually excited her a little. But whether she was or was not pregnant, she really needed to talk to Booth about their current situation.

The timer went off. This was it, the moment that could change her and Booth's lives forever. Brennan took a deep breath, and then looked at the three tests. All of them were positive.

The first feeling that registered was happiness. Pure, simple happiness. She was having a baby. Although she had only ever rationally explained the benefits of having a child, she had never voiced her desire to have a child born out of love. It was a desire that had grown over the last few years, as she had become more in touch with her emotions and had truly begun to realize what a beautiful thing it was to start a family. The problem in her situation, however, was that she may not have that family after all. Not if Booth had let go of the idea that they would ever get together. Sure, he had said that he would wait and would not give up on her, but she had broken his heart before. A man could only take so much.

Brennan decided not to tell Booth immediately. She wasn't really sure how to bring it up, and she feared his reaction a little. First, she would try to casually bring it up and see how he reacted to that, so she could reasonably brace herself for the actual conversation. Yes, that was what she would do. And with that in mind, she put on her undercover clothes and went to meet Booth.

* * *

As it turned out, it wasn't easy casually bringing up the topic of having babies. So when Brennan was going through Amber's laptop, she decided she would first try it with her dad. After all, if she tried it first with Booth and he sensed something was up, she would have to explain herself right there. And Brennan figured that since her dad didn't know she slept with Booth, he couldn't possibly figure out she was pregnant.

"If Buck and I ever have a child, she will not turn out like Amber!" There, that was quite casual, it fit perfectly into the current conversation. Brennan was pleased with herself. If she could similarly bring up the topic when talking to Booth, everything would be fine.

"You know, Temperance, it's just us monkeys now. You don't have to keep up your cover story."

Did Max realize that this was not actually about Amber? Did he know more about Booth and her than she had realized? Whatever it was that he did or didn't know, Brennan had to react quickly so as not to raise any further suspicions.

"I find it helpful to remain in character." She immediately went on about what she was seeing on Amber's laptop, not giving Max the chance to reply. He didn't interrupt her asking questions, so she was safe for now at least. But she still had to find out what Booth would think.

Not much later, an opportunity presented itself for Brennan to bring up having children. She and Booth were talking about Amber, and she figured she could make a similar bridge to the topic like she had done with her father.

"If we ever had a child like that Buck…"

"Oh, that's never ever gonna happen, Wanda. Never."

Well, that was a quick and sure answer, and it worried Brennan. What if Booth, too, was not just referring to Amber? What if he didn't ever want children with her, or couldn't even see them being together in an intimate relationship? It hurt to think that might be the case, but Brennan knew she had to brace herself for the possibility that she and Booth were not going to have the happy ending she had envisioned. Unfortunately, she could not find out for sure right now, as they had a murderer to catch.

* * *

Later, when they were in the waiting room of the hospital waiting for Hodgins to come out with his and Angela's child, Brennan couldn't help but think that she would be in a similar situation in about 8 months or so. The thought of having a child of her own excited her, but she would only be truly happy if she would have Booth by her side, which still remained to be seen.

When Hodgins exited the delivery room with his son, Brennan briefly caught Booth's eyes. She smiled at him and he smiled back, and in that moment she thought that maybe, just maybe, everything was going to be alright after all.

Brennan snuck away from the group admiring Michael Vincent, and went to see Angela. She thought that her friend might appreciate the company, but she also had a question for the new mom.

"What was it like?" She asked.

"It was wonderful, and beautiful. It was a dream," came the happy response from her friend.

Brennan was truly happy for Angela, but she couldn't help but feel worried again, despite having had that hopeful eye contact with Booth earlier. Having a baby was indeed supposed to be wonderful and beautiful, but what if it was not going to be like that for herself? If Booth wasn't going to be happy about the baby, or did not want to be in a relationship with her, she wasn't sure that she would be able to be truly happy. Brennan liked to think of herself as a strong, independent woman, but she could also recognize her flaws, especially concerning social interaction and becoming more in touch with her emotions. For that, she needed Booth by her side. Not just as a co-parent or a work partner, but as a life partner. The worrying was killing her, so made up her mind to tell Booth that night. She needed to know what to expect from the next months, or even years, of her life.

* * *

When Booth and Brennan left the hospital, there seemed to be some sort of unspoken understanding that tonight, they were finally going to talk for real. Of course, Booth did not know that it was going to be about more than just their relationship status. They walked out together, heading to Booth's apartment. Although Brennan had planned to tell Booth about her pregnancy once they got to his place, she suddenly couldn't bear to wait any longer.

"They looked so happy," she started.

"Yeah, well, they had a baby," he replied. He said it as if having a baby always resulted in happiness, no matter the circumstances. Would he feel that way too once she told him?

"Their whole lives have changed, you'd think they'd be a little more apprehensive."

"Well, you know, having a baby, that's a good thing."

It seemed more and more likely that Booth would be happy about having a baby, but Brennan was still nervous. "You- you really think that?" She asked.

"Yeah, it's a great thing, why?" he answered. Then he saw the worrisome look on her face. "What? Oh, come on, Bones. Look, the baby- the baby is fine, it's healthy, they had a healthy baby. Alright? They love each other, this is the happiest day of their lives, okay?"

He must have seen that she still had something on her mind. "What?" he asked again.

This was it, she had to tell him. No backing out now.

"I'm- I'm pregnant," she eventually said. She awaited his reaction, but he looked… confused? Maybe she should clarify further. "You're the father," she then added.

Still, only confusion on Booth's face, and a bit of shock. And then, finally, that beautiful smile of his. Brennan couldn't help but smile back at him.

"Oh, Bones, come here," Booth said, and wrapped his arms around her in a big hug. "A baby, huh? That's amazing!" Then something dawned on him, and he pulled back a bit so he could look into her eyes. "Wait, when you asked if I really thought that having a baby was a good thing, did you not expect that? Did you think I wasn't going to be happy about this?"

The look on her face told him enough, and Booth sighed. "Okay, come on, let's go inside. I have a feeling there is a lot we need to talk about, and I don't want to do that out here on the street." He started walking again, and Brennan hurried to catch up with him. Once she was beside him again, she slipped her hand in his, hoping that the small gesture was enough to settle his mind for now.

* * *

Once they got inside, Booth gently took Brennan's coat off and put it away for her. Brennan smiled at that. Whether or not he was a little miffed about her seeming lack of faith in him, he still remained a gentleman.

They both sat down on the couch and turned towards each other. Booth spoke first. "Did you really think I was not going to be happy about us having a baby together?"

"Well, after that night, when we, you know… we said we would talk about us, but before we had the chance, I shut down and distanced myself from you. I really did mean to take just a little time to think things through, but at some point I just didn't know how to bring it up. Then things got awkward and I figured that maybe you got tired of waiting. I wouldn't have blamed you if you did, I already crushed your heart once before. And when I found out I was pregnant, and I just didn't know how you would react. I was afraid that you were no longer interested in starting a relationship with me, let alone raising a child together."

Booth took both Brennan's hands in his. "Bones, when I said I would wait for you, I meant it. There is someone for everyone, and you're that someone for me. I am ready to give this relationship a try if you are."

"Yes, I think I am," Brennan replied. "But I need you to know that you should not feel any obligation to be with me just because I am carrying your child. I would never ask that of you."

"Hey, I know that. I love you, and I want to be with you. And sure, we didn't plan on having a baby right away, but that doesn't mean I'm any less happy about it. In fact, I am thrilled!" He put one of his hands on her still flat belly. "That is our bundle of joy in there. We are going to raise a child together, and there is nothing more beautiful than that, okay?"

Brennan smiled and put her hand over his on her belly. "Okay."

Booth kissed her once quickly, and then once more, a little longer this time. "Great! Now, no more worries, okay? And if something does bother you, you come to me. That's what I'm here for. We're going to figure this out together."

"I will try Booth, I promise," Brennan replied. Then she yawned.

"Yeah, you better," Booth said with a laugh. "And what you're also going to try is get some sleep right now, because apparently you and our baby need some rest."

Our baby. That sounded so good. Booth stood up and stretched out his hands to help Brennan get up. As they walked to the bedroom, Brennan realized that something else had sounded good too. "Booth, do you really love me?"

Booth stopped and turned to her, softly kissing her. "Of course I love you, Bones," he said, and then bent down to press his lips to her belly. "And I love our baby, too."

As they continued to the bedroom, Brennan couldn't help but feel happy. Although all of her worries and insecurities had not completely disappeared, Booth loved her and they were going to raise this baby together.

They were going to be just fine.

* * *

 _So, this was it, my first story after a long break from writing._

 _I immensely enjoyed writing this story, as I got to fully emerge myself in the world of Bones again. I never quite stopped re-watching it, but I feel a new kind of energy to watch it more, and to look at it with a different perspective. And who knows, maybe I'll get some more inspiration from other episodes and write a new Bones story soon (that is, once my midterms are over and I am no longer stressed out of my mind). I am currently re-watching Castle though, and watching a bunch of other shows as well, so maybe I'll write something else first._

 _In any case, thanks for reading, and perhaps till next time!_


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